I will keep it generic to both WTC1 and WTC2.
(Two disclaimers:
1) I have edited the following explanation from one posted several times since 2008 on other forums; AND
2) In the interest of clarity I will also take several
simplifying
short
cuts in the explanation. To stave off much of the 'let's prove him wrong' counter attacks I will label each such short cut thus
'SSC#1' 
)
The Context
At the start of the global collapse there was interaction between the bottom side of the Top Block AND the top side of the lower tower. And those two objects had this structure
...note the tube of outer wall columns, the core with multiple columns and cross braces and the open floor space resulting from the intentional adoption of the so called 'tube in tube' design. So the global collapse has to account for the interaction between the top block and the lower tower which are mirror reflections of each other and up till shortly before the initial collapse had been connected together.
There are three main questions:
1. What did the falling outer tube columns of the Top Block interact with and with what result?
2. How did the falling floor area interact with the floor area of the lower tower; AND
3. Ditto for the cores - how did the falling bit interact with the lower bit.
Set to one side for now the issue that the two blocks could not be perfectly aligned. It makes no significant difference.
'SSC#1'
What Happened with the Outer Tube?
It is clear that at some stage the Top Block broke up into its component parts. Where and precisely how that happened makes no difference for reasons which should become apparent.
The key factor is that as it fell the Top Block fell inside the outer tube of the lower Tower. And it appears that the outer columns of the top block were still attached at that stage which leads to the conclusion that those top block outer columns fell down inside the lower towers outer walls together with the floors and remainder of the top block. Either that or those top block outer columns fell outside the lower tower and were peeled off. As the global collapse progressed the outer tube columns of the lower tower were simply peeled off as the falling mass separated the floor joists from the columns. That part at least should be free of contention.
What happened to the Open Office Floor Areas?
Easy one. They fell onto the open floor areas of the lower tower. Whether still part of an integral Top Block or as components which had been disconnected. And it matters not which.
'SSC#2' If they fell as an integral block they would apply a load which was a significant portion of the Top Block weight. At later stages it is more likely that the falling load in the open floor area was the by now disconnected top block floors plus the accumulation of other floors as those floors were sheared of the columns. bottom line is that the falling mass sheared off the floors in sequence leaving the outer columns to fall over and the core columns with reduced horizontal restraint.
What happened to the core?
The key issue here is that by the time we entered this 'global collapse' stage all the core columns have failed and are not aligned 'top bit' sitting on 'bottom bit'. And even if some are still in that apposition the column has lost its load bearing capacity. So the wire basket of the top block core falls on the wire basket of the lower tower core.
And the key point is 'What part of the top block core strikes what part of the lower tower core?' It is not column on columns and must be the horizontal cross beams that land beam on beam and not in synchrony.
'SSC#3' The column 'end for end' contact had been displaced by the mechanism of the initial collapse. These beam on beam contacts are staggered in time. The dynamic, elastic and plastic factors make exact descriptions difficult to say the least BUT the first impact is one cross beam hitting another OR at the most a few such impacts at near enough to the same time. AND almost the total weight of the Top Block Core lands on one two or three beams.
The key descriptor is 'overwhelming'. The dynamic impact of 10 or 20 stories of core landing on a few cross beams
'SSC#4' will probably shear those beams at their shear critical point - probably the beam to column connection. And, if the beams yield in bending before failing they will drag columns out of alignment. As the collapse progresses falling material will impact columns as well as beams, columns already out of alignment. The interactions become far more complex BUT with one characteristic. It is not possible
'SSC#5' for true 'end for end' contact to be established which can develop the full load capacity of any one column. And even if it was for one column the falling weight is sufficient to instantly crush/buckle that one column into failure. The key concept at the start of global collapse is that the impact is of most of the weight of a 10 or 20 storey block dynamically applied to a few cross beams. Yes then a few more but never all at once in synchronism. And from that initial point contact with columns will be glancing contact against out of vertical struts leading to easy failure.
Now so far I have treated the collapse as outer tube on but actually missing outer tube; floor area on floor area and core on core. And all of those impacts involve overwhelming forces. If pure floor on floor it puts the total structure of 10 or 20 floors onto a floor designed to hold one floor. And the load is applied with dynamic impact. Failure is a foregone conclusion.
In reality the three components are joined - by the hat truss at roof level and by floor joist to column connectors at each floor of the top block. Those in interconnections would adjust the balance of where each bit of load was actually born but the falling mass landing on weak structural elements remains "overwhelming'.
And the key point to notice is that from the start of the global collapse stage the Top Block falls inside the outer tube of columns. Set aside for the moment the question of how it got wedged inside the lower tube.
'SSC#6' It is clear from just about every video of the collapse that the falling mass fell inside the outer tube of columns. And it is clear from the many photos of the outer tube columns lying scattered outwards from the tower that those columns had not been crushed end for end. They had simply been peeled off.
Summarising
Once the Top Block started to fall "global collapse was inevitable" to echo the words of NIST.
Inevitable because the strength of the outer tube of columns was bypassed. Because, once started with the separated columns not in alignment the strength of the core was mostly bypassed. The weights landing on the floor areas - many floors on one floor impacts and the weights landing on the core - many floors total weight landing mostly on the cross beams of one floor level of the core. Both areas saw structural elements overwhelmed by loads which as simple statically applied loads would have been at least a decimal order of magnitude higher than those elements were intended to support AND those loads applied dynamically further multiplying the gross overload.